tbuckley/cabot-search huggingface dataset:
Abstract 2701: Multivariate transcriptome analysis identifies networks and key drivers of metastatic castration-resistant prostate cancer
Authors: Lawrence P. McKinney, Rajesh Singh, I. King Jordan, Sooryanarayana Varambally, Martin G. Sanda, Eric B. Dammer, James W. Lillard
Journal: Cancer Research (2022)

Abstract Prostate cancer (PCa) is the second most cancer-related cause of death in men. Most PCa are characterized as slow-growing or indolent, though some patients are at a high risk of for recurrent and eventually metastatic disease. The most lethal form of PCa is metastatic castration-resistant prostate cancer (mCRPC) that has progressed to the bone. The molecular mechanism underlying PCa progression to bone has not been fully elucidated. Here, we identify gene networks associated with CRPC bone metastasis and survival risk. Networks were investigated by using a novel weighted gene network co-expression analysis (WGCNA) method and examining overrepresentation of upstream regulators and signaling pathways within co-expressed transcriptome modules across clinically annotated transcriptomes from mCRPC patients (N=60). Functional Enrichment analysis was used, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction analysis, to identify biological functions of related hub genes overrepresented in our module of interest. WGCNA identified that cyan module was significantly associated with castration-resistant prostate cancer (CRPC) bone metastasis. KEGG and GO analysis results revealed genes in blue module were mainly related to collagen formation, cell signaling peptides, and bone regulation processes, including alkaline phosphatase, osteoblast formation, and endochondral ossification. Genes positively correlated with bone metastasis exhibited the following biological pathways: PI3K-Akt signaling, ECM-receptor interaction, and protein digestion and absorption pathways. This study provides novel insights into the biological pathways associated with CPRC metastasis to the bone. The module associated with bone metastasis and overall survival represent both known and novel pathways. Citation Format: Lawrence P. McKinney, Rajesh Singh, I. King Jordan, Sooryanarayana Varambally, Martin G. Sanda, Eric B. Dammer, James W. Lillard. Multivariate transcriptome analysis identifies networks and key drivers of metastatic castration-resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2701.
Abstract 1219: Unraveling alternative polyadenylation in prostate cancer with CORE-PAD
Authors: Eddie L. Imada, Christopher Wilks, Ben Langmead, Luigi Marchionni
Journal: Cancer Research (2022)

Abstract Mechanisms that control gene expression at the RNA level are often referred to as post-transcriptional regulation (PTR) mechanisms. Splicing and polyadenylation (PA) are well-known examples of PTR that can regulate not only gene expression but also their function. Alternative Polyadenylation (APA) has already been shown to be essential to many biological processes (e.g., proliferation, cell differentiation, etc) and has also been implicated in the development and progression of multiple diseases (e.g., cancer, hematological and immune disorders, etc.). Although several sequencing methods have been developed to sequence only the transcript termination site (TTS), the number of publicly available data derived from these methods is extremely limited in comparison to traditional RNA-Seq data. To overcome this limitation, we created a new framework - Compositional Regression of Polyadenylation Differences (CORE-PAD) - for the study of differential APA events using traditional bulk RNA-seq data. Through simulated data, we showed that CORE-PAD has higher accuracy than other methods (accuracy = 0.98) in detecting APA events. We applied CORE-PAD across prostate cancer (PCa) samples with impaired CDK12 and “wild” samples. We found multiple genes presented differential PA site usage, including DNA repair genes. Most notably, we notice that many genes that exhibit differential APA were not differentially expressed at gene level, meaning they are potentially “silent drivers” that cannot be capture through standard differential gene expression analysis. These findings highlight the importance of studying APA, which can help shed light into another layer of regulation occurring between transcription and translation. This is especially important since these events can be source of neoantigens or targeted mRNA degradation which could be explore for new treatments. Finally, the CORE-PAD framework was designed to take advantage of our recently published recount3 resource making over 750,000 RNA-Seq samples of human and mouse origin readily available for analysis, enabling studies of APA across thousands of phenotypes in an accurate and accessible way. Citation Format: Eddie L. Imada, Christopher Wilks, Ben Langmead, Luigi Marchionni. Unraveling alternative polyadenylation in prostate cancer with CORE-PAD [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1219.
Abstract 2064: Targeting Cblb-Notch1 axis as a novel strategy for cancer immunotherapy
Authors: Giulia Monticone, Fred Csibi, Silvana Leit, Jermaine E. Austin, Deniz A. Ucar, Fokhrul M. Hossain, Samarpan Majumder, Barbara A. Osborne, Christine Loh, Lucio Miele
Journal: Cancer Research (2022)

Abstract Background: Tumor-induced immunosuppression is a way in which cancers evade the host immune response. In recent years, a great effort has been made in designing immunotherapies that can boost the immune system response against cancer. However, not all tumors respond to these therapies. Therefore, there remains an unmet need for immunotherapies that are able to circumvent tumor-induced immunosuppression. Adenosine is an immunosuppressive metabolite which is overproduced in hypoxic tumor microenvironments and dampens T-cell anti-tumor immune responses. Adenosine A2A receptor (A2AR) activation was shown to downregulate Notch1, a key regulator of T-cell functions, in CD8+ T-cells, leading to immunosuppression. Notch1 signaling appears to protect T-cells against immunosuppressive signals, as Notch1 overexpressing T-cells were shown to be resistant to tumor-induced immunosuppression mediated by myeloid-derived suppressor cells (MDSC), as well as adenosine. We hypothesize that rescuing Notch1 from downregulation will make T-cells resistant to tumor-induced immunosuppression. We applied several functional assays in primary CD8+ T-cells and tumor-derived organoids to study how Notch1 is regulated by A2AR and explore strategies to target this pathway for cancer immunotherapy. Results: Our results indicate that the ubiquitin ligase Cbl-b, a negative regulator of T-cell functions, is responsible for the ubiquitination and degradation of Notch1 in CD8+ T-cells. A2AR signaling leads to Notch1 downregulation by promoting Cbl-b-mediated Notch1 degradation. Inhibition of Cbl-b using small molecule compounds restores Notch1 and T-cell functions in CD8+ T-cells in the presence of adenosine, making them resistant to A2AR-mediated immunosuppression. Cbl-b inhibitors show anti-tumor activity in tumor-derived organoids from pre-clinical models and enhance immune-checkpoint immunotherapy, by promoting T-cells anti-cancer responses. Conclusions: Our work suggests that promoting Notch1 signaling by blocking Cbl-b-mediated degradation results in increased T-cell responses and resistance to immunosuppression. Targeting Cbl-b-Notch1 axis represents a promising novel strategy to boost anti-cancer T-cell responses. Citation Format: Giulia Monticone, Fred Csibi, Silvana Leit, Jermaine E. Austin, Deniz A. Ucar, Fokhrul M. Hossain, Samarpan Majumder, Barbara A. Osborne, Christine Loh, Lucio Miele. Targeting Cblb-Notch1 axis as a novel strategy for cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2064.
Abstract 1019: Address breast cancer equity through virtual community oncology navigation and engagement (vCONET)
Authors: Manisha Salinas
Journal: Cancer Research (2022)

Abstract The objective of this study is to develop and test a culturally sensitive, inclusive, and accessible virtual navigation model for Black women to promote and improve breast cancer screening behaviors. Breast cancer is among the leading causes of cancer morbidity and mortality globally, and there is a wide range of racial and ethnic disparities across the cancer continuum. Black women continue to have disproportionately high mortality rates compared to Whites, and are more impacted by triple-negative breast cancer and inflammatory breast cancer earlier in their lives and at more advanced stages. Patient navigation, particularly when culturally tailored to the intended population, is highly effective in reducing the complexity of access to care for cancer prevention and treatment. The growing momentum and usage of telehealth and virtual care has significant potential to reach Black women, to promote higher mammography screening and early detection of breast cancer. Virtual patient navigation can provide a safe, engaging, and accessible space to accelerate the application of practical approaches to address health disparities and increase preventive behaviors in underrepresented community. However, limited information exists on specific factors which impact the design, implementation, and receptivity of virtual navigation in Black communities. This study aims to: 2) Develop and test a culturally-adapted prototype of a virtual patient navigation intervention tool for increasing access to breast cancer screening education and promotion for Black women. 1) Use qualitative focus group methodology to explore the beliefs, attitudes, perceptions, and receptivity of community members of program usability and breast cancer awareness, prevention and screening behaviors among Black women. The study will examine social determinants of health that impact potential challenges to access utilization of mammography screening services. Qualitative focus group discussions will be conducted to guide the details of the virtual patient navigation, such as communication channels, specific messaging approaches, and sociocultural factors to integrate, as well as addressing current challenges and needs faced by the community. The results of this study can provide valuable insight to specific needs regarding outreach and access to screening mammography services to underrepresented communities of color to ultimately reduce breast cancer rates. Data collection is ongoing and preliminary results will be presented. Citation Format: Manisha Salinas. Address breast cancer equity through virtual community oncology navigation and engagement (vCONET) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1019.
Abstract 3837: The physiological relevance of TIMP dimer formation
Authors: Carolyn Lazaroff, David Peeney, Sadeechya Gurung, William G. Stetler-Stevenson
Journal: Cancer Research (2022)

Abstract Tissue inhibitors of metalloproteinases (TIMPs) are a family of four paralogous genes that modulate the activity of matrix metalloproteinases (MMPs) and are vital for tissue homeostasis. Additionally, TIMPs display activities that are independent of their MMP inhibitory activities. Dysregulation and perturbations within this system can lead to complex tissue-specific pathologies. TIMP2 is the most abundantly expressed member of the TIMP family and has been shown to display potential therapeutic uses in cancer and other diseases. We have noted the persistent presence of SDS-stable TIMP2 dimers/multimers in SDS-PAGE at a level of ~5% total protein. The goal of this study is to determine the stability and biological relevance of SDS-stable dimer formation of TIMP2 in in vitro and in vivo. We found that TIMP2 dimers display an enhanced ability to inhibit MMP2 activity in reverse zymography assays. Immunoblotting revealed gel extracted TIMP2 dimer entered an equilibrium with monomeric TIMP2, while the extracted monomer did not form new dimer. In addition, MMP2 activity assays do not corroborate the enhanced MMP2 inhibitory activity observed in reverse zymograms but are consistent with the observation that isolated TIMP2 dimers re-equilibrate with monomers. This implies that structural or sequence difference mediates the formation of dimers. Dimer/multimer formation is observed across the TIMP family. Mass spectrometry analysis of gel extracted TIMP monomers and dimers show that monomer and dimer forms of TIMPs display unique post-translation modification (PTM) profiles. We propose that understanding the interplay between TIMP multimers and PTMs will reveal new biological functions within this intriguing family of proteins. We are currently working to resolve the functional differences between monomer and dimer and reveal the underlying mechanisms at play. Citation Format: Carolyn Lazaroff, David Peeney, Sadeechya Gurung, William G. Stetler-Stevenson. The physiological relevance of TIMP dimer formation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3837.
Abstract 2826: Rewiring CAR T-cells for absolute solid tumor specificity and safety
Authors: Michael R. Weist, Adi Sharbi-Yunger, Jason Yi, Caitlin Schnair, David Bassan, Tanya Kim, Sarit Tabak, Yael Lopesco, Leehee Weinberger, Nir Bujanover, Neta Chaim, Kristina Vucci, Orit Foord, Frank J. Calzone, Rick Kendall, Gregor B. Adams
Journal: Cancer Research (2022)

Abstract Translation of the unprecedented efficacy of chimeric antigen receptor (CAR) T-cell technology into solid tumors requires a solution to the problem of on-target damage of vital organs. We have developed an inhibitory CAR platform (iCAR) that imposes self-regulation in CAR T-cells to restrict inappropriate activation against normal cells without compromising tumor efficacy. The system consists of an iCAR that is co-expressed with a conventional activating CAR (aCAR) designed to activate T-cells. The iCAR and aCAR scFvs bind distinct cell-surface antigens that are ubiquitously expressed across all solid tumor histologies and normal tissues. The iCAR is allele-specific whereas the aCAR is pan-allelic. The iCAR technology was validated in functional assays and NSG models with cancer cell lines that mimic loss-of-heterozygosity (LOH) which is common in most human cancers due to increased chromosomal instability. In this context, loss of iCAR target expression due to LOH generates irreversible target specificity. Tumor-specific overexpression of aCAR and iCAR targets, a common barrier to the clinical translation of potent agents targeting the cell-surface proteins is not required. We have shown using in vitro and in vivo models that CAR T-cell activation and target killing are fully inhibited by dual iCAR + aCAR antigen engagement. This outcome validates the concept of iCAR-mediated protection of normal cells in vital organs. In contrast, tumors that mimic iCAR target LOH through CRISPR editing were fully eradicated with aCAR engagement alone. T-cell activation, proliferation, and cytotoxic activity after exposure to target cells lacking iCAR target antigen was found to be quantitatively indistinguishable from the results obtained with single input aCAR CAR T-cells. These results suggest that iCAR technology can enable treatment of cancer patients with solid tumors using CAR T-cells that maximize potency and efficacy by mitigating on-target CRS, neurotoxicity, and inevitable organ damage. The restriction of CAR T activation to the local tumor environment by iCAR-mediated self-regulation directly addresses a fundamental technology gap that cannot be solved by CAR T dosing or aCAR modification alone. Citation Format: Michael R. Weist, Adi Sharbi-Yunger, Jason Yi, Caitlin Schnair, David Bassan, Tanya Kim, Sarit Tabak, Yael Lopesco, Leehee Weinberger, Nir Bujanover, Neta Chaim, Kristina Vucci, Orit Foord, Frank J. Calzone, Rick Kendall, Gregor B. Adams. Rewiring CAR T-cells for absolute solid tumor specificity and safety [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2826.
Abstract 5487: An auristatin-based peptide-drug conjugate targeting Kita-Kyushu lung cancer antigen 1 for precision chemoradiotherapy in gastric cancer
Authors: Xiaotong Chen, Fangcen Liu, Xiaoxiao Yu, Lin Li, Jiayao Yan, Baorui Liu
Journal: Cancer Research (2022)

Abstract Gastric cancer is a worldwide health problem. Concurrent chemoradiotherapy (CRT) represents an important strategy to reduce recurrence and prolong survival for gastric cancer. However, non-targeted cytotoxic drugs capable of enhancing radiosensitization remain the main choice to be combined with radiotherapy, which has limited the anti-tumor efficacy of CRT by off-target side effects. Monomethyl auristatin E (MMAE) is a highly potent anti-tubulin agent and has been reported to act as an effective radiosensitizer recently. Kita-Kyushu lung cancer antigen 1 (KK-LC-1) is a cancer/testis antigen highly and exclusively expressed in multiple types of cancers including gastric cancer, representing a promising target for drug delivery. Previously, we identified a KKLC-1-targeting cyclic nonapeptide (1131 peptide) by screening a phage display peptide library. Here, we described a novel peptide-drug conjugate (PDC) 1131-MMAE by connecting the 1131 peptide with MMAE via a protease-sensitive linker for tumor-selective radiosensitization. We demonstrated that 1131-MMAE could be efficiently internalized by gastric cancer cells through KKLC1-mediating endocytosis and exhibited a comparable cytotoxicity profile with free MMAE. 1131-MMAE could arrest the cell cycle at the most radiosensitive G2/M phase in a dose-dependent manner and selectively enhance the radiation response of KK-LC-1 positive gastric cancer cells by increasing DNA double-strand break as indicated by γH2Ax immunofluorescence staining. Furthermore,1131-MMAE was able to inhibit tumor growth as a monotherapy at 2mg/kg with a good safety profile in vivo. Increased tumor control was achieved when 1131-MMAE was combined with radiotherapy at a relatively low dose of 0.3mg/kg. Overall, we proposed an MMAE-based PDC targeting a novel tumor marker KK-LC-1 and demonstrated its tumor-selective radiosensitization in gastric cancer models for the first time. This anti-KKLC1 PDC may help to promote the clinical progress in precision chemoradiotherapy for multiple types of cancer. Citation Format: Xiaotong Chen, Fangcen Liu, Xiaoxiao Yu, Lin Li, Jiayao Yan, Baorui Liu. An auristatin-based peptide-drug conjugate targeting Kita-Kyushu lung cancer antigen 1 for precision chemoradiotherapy in gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5487.
Abstract 4230: Modeling the cDC1 <i>ex vivo</i> and <i>in vitro</i>: Development and comparison of a conventional dendritic cell culture system for industry
Authors: Laura L. Goodfield, Johanna Lahdenranta, Heather Scott, Tamera Ashworth, Lia Luus, Anna F. Licht, Kevin McDonnell, Phil Brandish, Nicholas Keen
Journal: Cancer Research (2022)

Abstract Conventional dendritic cells (cDC) are innate immune cells specialized in antigen sampling and subsequent cross-presentation to immune cells and are critical for an effective anti-tumor immune response. While crucial to immunity against intracellular pathogens, viruses, and tumors, cDC type I (cDC1) are a relatively rare population and constitute about 0.05% of cells in the blood. Using these rare cells in screening assays can be a challenge, as very small proportions are found in peripheral human blood and since they are difficult to isolate with high viability and purity. Existing methods to generate acceptable numbers of cDC1s require a feeder cell line, which is not accessible to many laboratories. Using a systematic approach, we developed a scalable differentiation system to generate a mixed culture containing cDC1 cells from CD34+ hematopoietic stem cells isolated from cord blood that does not require feeder cells. This culture of cells has been phenotypically and functionally characterized to express high levels of CD141 and Clec9a, as well as responsiveness to various activating stimuli including poly (I:C). Cells derived from this culture method express similar levels of CD141 and Clec9a compared to those observed in peripheral blood of healthy donors. Our effort to find a less laborious, more efficient system includes comparison to cDC1 responses from an in vitro differentiation system to cDC1s isolated from humanized mouse bone marrow, with evaluation of both surface marker phenotype and responsiveness to activating stimuli. We also compared the responses of these cells to monocyte derived dendritic cells that express CD141 and Clec9a. These data demonstrate that the HSC-derived cDC1 cultures provide a comparison of unique dendritic cells that may be utilized for screening assays in an industry setting. Citation Format: Laura L. Goodfield, Johanna Lahdenranta, Heather Scott, Tamera Ashworth, Lia Luus, Anna F. Licht, Kevin McDonnell, Phil Brandish, Nicholas Keen. Modeling the cDC1 ex vivo and in vitro: Development and comparison of a conventional dendritic cell culture system for industry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4230.
Abstract 409: Reversal of ABCG2-mediated multidrug resistance by tepotinib <i>in vitro</i> and <i>in vivo</i>
Authors: Zhuoxun Wu, Qiu-Xu Teng, Yuqi Yang, Nikita Acharekar, Jing-Quan Wang, Min He, Sabesan Yoganathan, Jun Lin, Jian Wang, Zhe-Sheng Chen
Journal: Cancer Research (2022)

Abstract ABCG2/BCRP transporter-mediated Multidrug resistance (MDR) in cancers has been considered as one of the obstacles to the cancer chemotherapy. Our recent study characterized the MET inhibitor tepotinib as a potent ABCB1 inhibitor. In the present study, we demonstrated the MET inhibitor tepotinib effectively antagonized ABCG2-mediated MDR in vitro and in vivo. In addition, the ABCB1/ABCG2 double-transfected cell model demonstrated that tepotinib can simultaneously inhibit the two MDR transporters. Mechanistically, tepotinib stimulated ABCG2 ATPase activity without altering the protein expression level of ABCG2, MET, or p-MET. Moreover, the MDR reversal effect may be attributed to its reversible inhibition of ABCG2 substrate efflux function, thereby sensitizing the drug-resistant cancer cells to substrate drugs. The molecular docking analysis suggested that tepotinib may directly bind to the drug-binding site of ABCG2, which subsequently block the binding of ABCG2 substrates. Animal study showed that tepotinib significantly increased the intratumor accumulation of ABCG2 substrate drug topotecan and enhanced its antitumor effect in ABCG2-overexpressing tumors. In conclusion, our study provides a new strategy of repositioning tepotinib as an MDR modulator to antagonize ABCG2-mediated MDR. Citation Format: Zhuoxun Wu, Qiu-Xu Teng, Yuqi Yang, Nikita Acharekar, Jing-Quan Wang, Min He, Sabesan Yoganathan, Jun Lin, Jian Wang, Zhe-Sheng Chen. Reversal of ABCG2-mediated multidrug resistance by tepotinib in vitro and in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 409.